The flu has been making the rounds at commercial poultry farms since December, and to date, more than 38 million birds have been infected and killed as a result. Wisconsin, Minnesota, and Iowa have declared a state of emergency, and China and Mexico have imposed bans on US poultry and eggs.

In May, the US government approved $330 million in "emergency funds" to help fight the disease's spread.1 And the US Department of Agriculture (USDA) has also stepped in, with 266 employees dedicated to helping states affected by the outbreak. The Agency has also approved $130 million (of taxpayer money) to help CAFOs "get back on their feet."2

Avian flu is thought to have originated in wild birds, which then transferred the virus to the commercial flocks. But there's one peculiarity, which is that backyard poultry flocks have remained largely unaffected. As noted by Mother Jones:3

"Backyard flocks typically roam outdoors, in ready contact with wild birds, which are thought to be the origin of the virus. Their commercial counterparts live in tight confinement under strict 'biosecurity' protocols: birds are shielded from contact with the outdoors; workers change into special boots and coveralls—or even shower—before entering facilities, etc."

There are some theories as to how bird flu has managed to get past CAFOs' "biosecurity" protocols. USDA Secretary Tom Vilsack has suggested the virus may be entering through biosecurity breaches, such as using potentially contaminated pond water to feed and water CAFO birds, or workers neglecting to shower before entering the facility.4

Hon S. Ip, a virologist at the US Geological Survey's National Wildlife Health Center, said the CAFO birds might come into contact with infected feces from wild birds or through wind-borne particles that blow through CAFO vents. This latter theory would imply that backyard flocks would be similarly affected, but they are not.5

Even the journal Science has called this particular bird flu "enigmatic,"6 and Michael Osterholm, director of the Center for Infectious Disease Research and Policy at the University of Minnesota, said:7

"All the old dogma about high-path influenza transmission has just gone out the window… We're in totally uncharted territory."

But for all of the apparent mystery, there seems to be a basic explanation for why CAFO birds are getting sick while their wild counterparts are spared. It has nothing to do with the animals; it's how they're being raised that's the problem.

Disease Runs Rampant Among Unhealthy, Stressed Animals

What happens when you have tens, or even hundreds, of thousands of animals living together in cramped, waste-covered quarters, fed an unnatural and unhealthy diet, and unable to spend time outdoors or engage in any of their natural behaviors? Disease takes hold and runs rampant. As reported in the journal Environmental Health Perspectives:8

"As a general principle, the concentration of humans or animals in proximity enhances potential transmission of microorganisms among members of the group.

It also creates greater potential for infecting surrounding life forms, even those of different species. The conditions created also may be a breeding ground for new, more infectious, or more resistant microorganisms."

Aside from their close quarters, these animals are literally living in their own waste, furthering the spread of disease. According to CAFO: The Book:9

"The world's tens of billions of meat chickens—'broilers'—grow at a freakishly fast pace. Concentrated in houses with upwards of 20,000 to 30,000 other birds, each full-grown chicken gets less than a square foot of living space. Modern broilers spend their short 7-week lives on top of their own waste encrusted bedding,

…Inside the scrambled priorities of an industrial egg laying facility, most hens are confined in wire 'battery cages' like egg producing slaves, often with no room to move or even flap their wings without touching another bird.

Their beaks are regularly seared off so they can't kill or maim one another. They lack even a shred of privacy to lay their eggs, a condition that can cause great distress."

Stressed animals are also more vulnerable to disease, and this doesn't even take into account the fact that many CAFO animals are routinely fed low doses of antibiotics. This excessive exposure to antibiotics poses a great risk to the spread of antibiotic-resistant disease and also takes a heavy toll on gastrointestinal health. This in turn can predispose animals to virtually any disease.

In contrast, wild animals are allowed to eat their native diets. They're not forced to stay within inches of other animals for their entire lives, and they're not typically living in their own waste. Disease can certainly spread in the wild… but when it does it's generally self-limiting. The diseases don't typically spread like wildfire the way they do in CAFOs, wiping out millions of birds in a matter of months…

Could Bird Flu Spread from CAFOs to Humans?

Although avian flu doesn't spread easily among humans, its capability to mutate has scientists worrying whether it could mutate enough to cause a human pandemic. CAFOs serve as the ideal place for this to happen, as there are millions of host birds among which the virus can flourish.

In Iowa, for instance, CAFOs house an average of 60 million egg-laying hens.10 Iowa is the top egg-producing state in the US, and it's been among the hardest hit by the avian flu outbreak. About 40 percent of the egg-laying CAFO flocks in Iowa have been wiped out.11

In the Netherlands, animal health authorities recently discovered bird flu in samples taken from wild ducks.12 In that case, chicken farms were suspected as the source of the disease.

There is also already evidence of antibiotic-resistant superbugs "jumping" from farm animals to people. For instance, two human cases of infection with the antibiotic-resistant superbug MRSA were linked to livestock in Denmark.13 As reported by Mother Jones:14

"The Danish study comes on the heels a 2012 paper by a consortium of US and European researchers, which used gene sequencing to show that another common strain of MRSA originated in humans as a common staph infection, jumped to livestock, where it evolved resistance to the common antibiotics tetracycline and methicillin, and then jumped back to humans.

Of course, you can also contract antibiotic-resistant pathogens through contact with raw meat—as, for example, more than 100 people did when the agribusiness giant Cargill sent out tens of millions of pounds of ground turkey tainted with antibiotic-resistant salmonella in 2011."

Outbreaks of Antibiotic-Resistant Disease Could Be Even Deadlier

Nearly 25 million pounds of antibiotics are administered to livestock in the US every year for purposes other than treating disease, such as making the animals grow bigger faster. In fact, 80 percent of the antibiotics used in the US are used in agriculture, and this practice is promoting the spread of antibiotic-resistant disease. As reported in Environmental Health Perspectives:15

"This prolonged use of antibiotics, especially at low levels, presents a risk of not killing the bacteria while promoting their resistance by selecting for resistant populations. The resistance genes can pass readily from one kind of bacteria to another.

Thus, workers in the animal units may become colonized with resistant organisms and can pass them on to co-workers and family members or friends. Consumers of meat may also become colonized through mishandling of raw meat or through insufficient cooking. Ultimately, these genes may pass into pathogens, and diseases that were formerly treatable will be capable of causing severe illness or death."

Drug-resistant bacteria also accumulate in manure that is spread on fields and enters waterways, allowing the drug-resistant bacteria to spread far and wide and ultimately back up the food chain to us. Now, we're facing a crisis. Antibiotic-resistant bacteria infect 2 million Americans every year, causing at least 23,000 deaths.16

Worse still, a report commissioned by UK Prime Minister David Cameron estimates that by 2050 antibiotic resistance will have killed 300 million people, with the annual global death toll reaching 10 million.17 And according to the CDC, 22 percent of antibiotic-resistant illness in humans is in fact linked to food,18 but a more accurate statement might be linked to food from CAFOs.

Where are the Millions of Infected Carcasses Being Disposed Of?

When millions of infected birds are killed off in one fell swoop, disposing of the carcasses becomes a public-health issue in and of itself. Sometimes the carcasses are turned into compost on-site, a process that takes weeks but which will likely prove impractical for farms dealing with millions of birds. The birds could also be buried on-site, but this poses issues with millions of decomposing birds contaminating groundwater. Another option is to transport the carcasses to a landfill or rendering facility, which pose risks of their own. As reported by CNBC:19

"Carcasses could be removed from the property altogether, presenting another challenge: transportation. Experts say off-site removal runs the risk of spreading the virus. Sealed trucks must be used, and their routes strictly limited to landfills or rendering facilities. Rendering is the process of converting animal tissue into "value-added" products—everything from pet and livestock feed to biofuels and detergent."

While the bird flu virus doesn't survive long after the host animal dies, there's the potential that some virus would remain during transportation. Meanwhile, many landfill operators are reluctant to accept millions of infected birds, citing environmental reasons (waste runoff often seeps into groundwater) and fears of contamination.20 CAFOs are already among the largest polluters in the US, and this bird flu epidemic is only adding to the environmental assault.

Will the Bird Flu Outbreak Cause Egg Shortages and Price Increases?

Many US food companies have already been affected by egg shortages as a result of the bird flu outbreak. One of McDonald's egg suppliers, for instance, was directly impacted, and other corporations, including Panera Bread and General Mills, are seeking out other suppliers or alternative ingredients, like plant-based egg substitutes.21

Other companies have made plans to begin importing eggs from Europe. The outbreak has cut US supply of "breaker eggs," which are liquid, dried, and frozen eggs used by food manufacturers, by close to 30 percent.

Such eggs are now selling for $1.83 a dozen, up from $0.63 cents a dozen in late April. "Shell eggs," which are the type sold by the carton in grocery stores, have also increased significantly in price. Wholesale costs rose from $1.19 a dozen in late April to $2.03 a dozen in late May.22 According to analysts at Goldman Sachs, consumers may end up spending up to $8 billion because of the bird-flu-induced egg shortage.

If you haven't already considered it, now would be a great time to connect with a local farm that offers healthy chicken and eggs. The products might be expensive than the CAFO versions at your grocery store… but are they really more expensive, all things considered?

Have You Thought About Starting Your Own Backyard Flock?

About the only better option to getting your eggs and chicken fresh from a small local farm is raising your own backyard flock. Backyard chickens are growing in popularity, and many US cities are adjusting zoning ordinances to allow for this pastime. Requirements vary widely depending on your locale, with many limiting the number of chickens you can raise or requiring quarterly inspections (at a cost) and permits, so check with your city before taking the plunge.

You might be surprised to find that your city already allows chickens, as even many large, urban cities have jumped on board (Chicago, Illinois, for instance, allows residents to keep an unlimited number of chickens, as "pets" or for eggs, provided you keep a humane and adequately sized coop).

For most people interested in raising backyard chickens, the greatest allure is the ready access to fresh, free-range eggs. Free-range or "pastured" organic eggs are far superior when it comes to nutrient content, while conventionally raised eggs are far more likely to be contaminated with disease-causing bacteria such as Salmonella.

You can usually tell your eggs are pastured by the color of the egg yolk. Foraged hens produce eggs with bright orange yolks, and this is what most people who raise backyard chickens are after. Dull, pale yellow yolks are a sure sign you're getting eggs from caged hens that are not allowed to forage for their natural diet.

Remember, too, that even if you don't want to raise your own chickens but still want farm-fresh eggs, you have many options. Finding high-quality organic, pastured eggs locally is getting easier, as virtually every rural area has individuals with chickens.

If you live in an urban area, visiting the local health food stores is typically the quickest route to finding high-quality local egg sources. Farmers' markets and food co-ops are another great way to meet the people who produce your food. With face-to-face contact, you can get your questions answered and know exactly what you're buying. Better yet, visit the farm -- ask for a tour. If they have nothing to hide, they should be eager to show you their operation.